The mammalian basic helix-loop-helix/PAS family of transcriptional regulators

A reinforced merging methodology for mapping unique peptide motifs in members of protein families

Background

Members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-D) structures. However, enzymes with high sequence identity may acquire differential functions other than the common catalytic ability. It is probable that each of their variable regions consists of a unique peptide motif (UPM), which selectively interacts with other cellular proteins, rendering additional biological activities. The ability to identify and localize such UPMs is paramount in recognizing the characteristic role of each member of a protein family.

Results

We have developed a reinforced merging algorithm (RMA) with which non-gapped UPMs were identified in a variety of query protein sequences including members of human ribonuclease A (RNaseA), epidermal growth factor receptor (EGFR), matrix metalloproteinase (MMP), and Sma-and-Mad related protein families (Smad). The UPMs generally occupy specific positions in the resolved 3-D structures, especially the loop regions on the structural surfaces. These motifs coincide with the recognition sites for antibodies, as the epitopes of four monoclonal antibodies and two polyclonal antibodies were shown to overlap with the UPMs. Most of the UPMs were found to correlate well with the potential antigenic regions predicted by PROTEAN. Furthermore, an accuracy of 70% can be achieved in terms of mapping a UPM to an epitope.

Conclusion

Our study provides a bioinformatic approach for searching and predicting potential epitopes and interacting motifs that distinguish different members of a protein family.

Primary Structure and Organ-Specific Expression of the Rat Aryl Hydrocarbon Receptor Repressor Gene

The aryl hydrocarbon receptor repressor (AhRR) is a member of the basic helix-loop-helix/Per-Arnt-Sim (bHLH/PAS) family of transcription factors, providing a negative feedback loop with a xenobiotic or endogenous ligand-dependent signal transduction mediated by the AhR. We sequenced full-length AhRR mRNA extracted from the heart of a male Wistar rat injected intraperitoneally with 3-methylcholanthrene (3-MC) 24 h before. The 95.6 kb-long AhRR genome was clarified to consist of 11 exons and 10 introns. The constitutive expression of AhRR mRNA was prominent in males when compared with females in parallel with the sexual difference in AhR expression. Although AhRR was ubiquitously expressed in all tissues tested, the levels of AhRR expression were higher in the small intestine, where the 3-MC-dependent induction of CYP1A1 transcription was less significant, than in the heart, lung, liver, and kidney. The dose-dependent suppression of AhR-dependent transcriptional activation in both the presence and absence of 3-MC was observed in rat liver-derived RL-34 cells transiently transfected with the expression plasmid for AhRR in combination with the reporter plasmid.

The circadian regulation of Presenilin-2 gene expression

Circadian rhythms are generated by a molecular clock composed of clock genes and their protein products. Other genes are regulated in a rhythmic way by this molecular clockwork, but are not themselves constituents of the clock. This study shows that one of these clock-controlled genes encodes the signalling protein Presenilin-2. Indeed, evidence is presented that the promoter of the mouse Presenilin-2 gene is bound and activated by CLOCK and BMAL1, transcription factors of the mammalian circadian clock. Quantification of Presenilin-2 RNA shows that its expression is non-rhythmic in many peripheral tissues (heart, muscle, kidney, spleen, and thymus). Note, though, that careful analysis of the liver data shows that Presenilin-2 RNA exists in distinct isoforms in this tissue, and that rhythmicity is restricted to only a subset of these RNA isoforms. These data indicate a unique mode of regulation of Presenilin-2 transcripts, the circadian control of which appears to happen at the transcriptional and post-transcriptional levels.

Cellular response to tissue hypoxia and its involvement in disease progression

Multicellular organisms show adaptive reactions for their survival when they are exposed to an atmosphere with reduced oxygen concentration. These reactions include increase in respiratory volume, switch from aerobic to anaerobic metabolism, erythropoiesis and angiogenesis. For these reactions, cells must change the expression of several hypoxia-responsive molecules such as erythropoietin and vascular endothelial growth factor. Hypoxia-responsible element (HRE) was delineated in the genes of hypoxia-responsive molecules as the sequence indispensable for their hypoxia-induced transcriptional activation, and hypoxia-inducible factor 1 (HIF-1) was identified as a transcriptional factor that binds to HRE and regulates the expression of various hypoxia-responsive molecules. Increasing evidence has revealed that HIF-1 is a key molecule regulating the cellular response to tissue hypoxia. HIF-1 is composed of two subunits, HIF-1alpha and HIF-1beta, and HIF-1 activity depends mainly on the intracellular level of HIF-1alpha protein, which is regulated to be in inverse relation to the oxygen concentration by an oxygen-dependent enzyme, prolyl hydroxylase 2 (PHD2). Thus, cells respond to tissue hypoxia by sensing the oxygen concentration as the enzyme activity of PHD2, regulating the HIF-1 activity and consequently changing the expression of various hypoxia-responsive molecules. Cellular response controlled by hypoxia-HIF-1 cascade is also involved in pathological situations such as solid tumor growth, diabetic retinopathy and rheumatoid arthritis. Under these pathological situations, the activation of hypoxia-HIF-1 cascade often leads to the acceleration of disease progression. Understanding an aspect of disease progression triggered by tissue hypoxia might provide a clue to new therapeutic strategies for intractable diseases.

Involvement of upstream stimulatory factor in regulation of the mouse Prnd gene coding for Doppel protein

Promoter of the Prnd gene coding for the Prion-like protein Doppel contains two critical cis-regulatory elements, NF-Y consensus motif and canonical E-box. Here, we studied a role of the upstream stimulatory factor (USF) in the E-box-mediated activation of Prnd transcription. Co-expression of USF-1 with the luciferase reporter gene driven by the -185/+27 Prnd promoter fragment resulted in several fold increase of the luciferase activity. Conversely, mutations within the E-box led to a significantly reduced Prnd promoter activation. USF-1 binding was supported by the gel shift assay, supershift with USF-1 antibody and UV cross-linking. The activation capacity of the related USF-2, c-Myc and HIF-2alpha proteins was lower compared to USF-1 suggesting that USF-1 is the major E-box-binding transcription factor regulating the Prnd promoter.

Role of the carboxy-terminal transactivation domain and active transcription in the ligand-induced and ligand-independent degradation of the mouse Ahb-1 receptor

To assess the importance of transactivation domains (TAD), DNA binding and transcription on the degradation of the AH receptor (AHR), Hepa-1 cells were pre-treated with actinomycin D (AD) or cycloheximide (CHX) and exposed to 2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD). AD or CHX did not affect nuclear localization or DNA binding of the AHR but inhibited ligand-induced degradation. In contrast, AD or CHX did not inhibit geldanamycin (GA) induced degradation of the AHR. To assess the role of the COOH-terminal TAD in AHR degradation, stop codons were placed at nucleotide 1501 and 1921 of the Ah(b-1) AHR coding region to generate AHR(500) and AHR(640). Stable cell lines were generated and exposed to TCDD. Cells expressing AHR(500) did not induce CYP1A1 protein, but exhibited significant degradation of AHR(500). Cells expressing AHR(640) induced CYP1A1 protein to 50% of the level of cells expressing wild type AHR and exhibited significant degradation of AHR(640). Importantly, AD and CHX did not inhibit the TCDD-induced degradation of either AHR(500) and AHR(640) and these receptors showed a more rapid profile of ligand-induced degradation compared to cells expressing wild type AHR. TCDD exposure to Hepa-1 cells with reduced aryl hydrocarbon receptor nuclear translocator (ARNT), showed ligand-induced degradation of the AHR that was not blocked by AD. However, AD inhibited TCDD-induced degradation when ARNT expression was restored. These results show that multiple mechanisms exist for the ligand and GA-induced degradation of the AHR and suggest that ligand-induced degradation can switch between two mechanisms depending on the presence of a functional TAD and the binding to DNA.

Abnormal neurodevelopment, neurosignaling and behaviour in Npas3-deficient mice

Npas3 is a member of the bHLH-PAS superfamily of transcription factors that is expressed broadly in the developing neuroepithelium. To study the function of this gene, mice deficient in Npas3 were generated and characterized. Npas3-/- mice were growth-retarded and exhibited developmental brain abnormalities that included a reduction in size of the anterior hippocampus, hypoplasia of the corpus callosum and enlargement of the ventricles. A number of behavioural abnormalities were identified in Npas3-/- mice including locomotor hyperactivity, subtle gait defects, impairment of prepulse inhibition of acoustic startle, deficit in recognition memory and altered anxiety-related responses. Characterization of neurosignaling pathways using several pharmacological agents revealed dysfunctional glutamate, dopamine and serotonin neurotransmitter signaling. Consistent with these findings, we identified a significant alteration in cortical PSD-95 expression, a PDZ-containing protein that has been shown to be involved in postsynaptic signal transduction. Together, our observations indicate an important role for Npas3 in controlling normal brain development and neurosignaling pathways.

Loss of ARNT/HIF1beta mediates altered gene expression and pancreatic-islet dysfunction in human type 2 diabetes

beta cell dysfunction is a central component of the pathogenesis of type 2 diabetes. Using oligonucleotide microarrays and real-time PCR of pancreatic islets isolated from humans with type 2 diabetes versus normal glucose-tolerant controls, we identified multiple changes in expression of genes known to be important in beta cell function, including major decreases in expression of HNF4alpha, insulin receptor, IRS2, Akt2, and several glucose-metabolic-pathway genes. There was also a 90% decrease in expression of the transcription factor ARNT. Reducing ARNT levels in Min6 cells with small interfering RNA (siRNA) resulted in markedly impaired glucose-stimulated insulin release and changes in gene expression similar to those in human type 2 islets. Likewise, beta cell-specific ARNT knockout mice exhibited abnormal glucose tolerance, impaired insulin secretion, and changes in islet gene expression that mimicked those in human diabetic islets. Together, these data suggest an important role for decreased ARNT and altered gene expression in the impaired islet function of human type 2 diabetes.

Cytokines and the regulation of hypoxia-inducible factor (HIF)-1alpha

Hypoxia-inducible factor (HIF)--an oxygen sensor? The HIF-oxygen sensing association type of dogma is, unequivocally, well anchored. But this is only one face of, at least, a double-sided coin. Current concepts charge HIF of taking sides with a yet not well-founded identity--an immunologic sensor and/or regulator. Or, is it really a sensor, put it more correctly, a key player in sensing mechanisms? The evolving association between HIF and immunity emanates from an established linkage that bonds oxidative stress and inflammation--notably the 'biologic response modifiers', or cytokines. HIF is a redox(y)-sensitive transcription factor, and so are cytokines. Recently, cytokines emerged as major regulators of HIF, under physiologic conditions extending the realm of hypoxia. Alternatively, can HIF, like the so infamous inflammatory transcription factor NF-(kappa)B, prove itself as a key player in the regulation of cytokines and, subsequently, the inflammatory process. The targeting of HIF would be, at least theoretically, of therapeutic value, but does it make sense given its intricate role in hypoxia signaling? It is the theme of HIF being an immunologic sensor that will be explored therein--with special emphasis on the regulatory role of cytokines.

Structural basis of ARNT PAS-B dimerization: use of a common beta-sheet interface for hetero- and homodimerization

The aryl hydrocarbon receptor nuclear translocator (ARNT) is a promiscuous bHLH-PAS (Per-ARNT-Sim) protein that forms heterodimeric transcriptional regulator complexes with several other bHLH-PAS subunits to control a variety of biological pathways, some of which are centrally involved in disease initiation and/or progression. One of these is the hypoxia response pathway, which allows eukaryotic cells to respond to low oxygen tension via the formation of a heterodimeric complex between ARNT and another bHLH-PAS protein, the hypoxia-inducible factor alpha (HIF-alpha). We have previously shown that the C-terminal PAS domains of an HIF-alpha isoform (HIF-2alpha) and ARNT interact in vitro, and that mutations in the solvent-exposed beta-sheet surface of the HIF-2alpha domain not only disrupt this interaction, but also greatly attenuate the hypoxia response in living cells. Here, we have solved the solution structure of the corresponding PAS domain of ARNT and show that it utilizes a very similar interface for the interaction with the HIF-2alpha PAS domain. We also show that this domain self-associates in a concentration-dependent manner, and that the interface used in this homodimeric complex is very similar to that used in the formation of heterodimer. In addition, using experimentally derived NMR restraints, we used the program HADDOCK to calculate a low-resolution model of the complex formed in solution by these two PAS domains, and confirm the validity of this model using site-directed spin labeling to obtain long-range distance information in solution. With this information, we propose a model for the mode of multi-PAS domain interaction in bHLH-PAS transcriptional activation complexes.

Characterization of nuclear localization signals and cytoplasmic retention region in the nuclear receptor CAR

The constitutive androstane receptor (CAR) is a ligand/activator-dependent transactivation factor that resides in the cytoplasm and forms part of an as yet unidentified protein complex. Upon stimulation, CAR translocates into the nucleus where it modulates the transactivation of target genes. However, CAR exogenously expressed in rat liver RL-34 cells is located in the nucleus even in the absence of activators. By transiently transfecting RL-34 cells with various mutated rat CAR segments, we identified two nuclear localization signals: a basic amino acid-rich sequence (RRARQARRR) between amino acids 100 and 108; and an assembly of noncontiguous residues widely spread over amino acid residues 111 to 320 within the ligand binding domain. A C-terminal leucine-rich segment corresponding to a previously reported murine xenochemical response signal was not found to exhibit nuclear import activity in cultured cells. Using rat primary hepatocytes transfected with various CAR segments, we identified the region required for the cytoplasmic retention of CAR. Based on these results, the intracellular localization of CAR would be determined by the combined effects of nuclear localization signals, the xenochemical response signal, and the cytoplasmic retention region.

Phosphorylation inhibits DNA-binding of alternatively spliced aryl hydrocarbon receptor nuclear translocator

The basic helix-loop-helix/PER-ARNT-SIM homology (bHLH/PAS) transcription factor ARNT (aryl hydrocarbon receptor nuclear translocator) is a key component of various pathways which induce the transcription of cytochrome P450 and hypoxia response genes. ARNT can be alternatively spliced to express Alt ARNT, containing an additional 15 amino acids immediately N-terminal to the DNA-binding basic region. Here, we show that ARNT and Alt ARNT proteins are differentially phosphorylated by protein kinase CKII in vitro. Phosphorylation had an inhibitory effect on DNA-binding to an E-box probe by Alt ARNT, but not ARNT, homodimers. This inhibitory phosphorylation occurs through Ser77. Moreover, a point mutant, Alt ARNT S77A, shows increased activity on an E-box reporter gene, consistent with Ser77 being a regulatory site in vivo. In contrast, DNA binding by an Alt ARNT/dioxin receptor heterodimer to the xenobiotic response element is not inhibited by phosphorylation with CKII, nor does Alt ARNT S77A behave differently from wild type Alt ARNT in the context of a dioxin receptor heterodimer.

Hypoxia-dependent activation of HIF into a transcriptional regulator

Adaptation to conditions of limited oxygen availability (hypoxia) is a critical determinant of cell and tissue viability in several physiological and pathophysiological conditions. The hypoxia-inducible factor (HIF) is an oxygen-sensitive transcriptional activator that, under hypoxia, upregulates the expression of genes involved in the control of glucose metabolism, angiogenesis and cellular proliferation, among others. Activation of HIF to a fully competent transcriptional regulatory protein complex is a multi-step process that involves control of protein stability, subcellular localization, DNA-binding and interaction with transcriptional coregulators. The identity, regulation and hierarchy of interactions between several components of the HIF signal transduction pathway has been the object of intense study over the past decade and will be the subject of this review. Particular emphasis is given to the process of coordinated coactivator recruitment within the cell nucleus. The implications for future development of angiogenic/antiangiogenic therapeutic strategies of HIF activation/inactivation are discussed.

Hypoxia-inducible factor 1 proteomics and diving adaptations in ringed seal

The putative amino acid sequence of ringed seal (Phoca hispida) hypoxia-inducible factor 1alpha (HIF-1alpha) derived from DNA sequence analysis of the single-copy gene has been investigated. The rationale for these studies was to determine the reasons for the presence of HIF-1alpha at relatively high levels in seal tissues, and its possible role in protection against diving-related oxidative damage. Sequence analysis indicated that the bHLH/PAS and TAD functional domains are very similar to those in terrestrial mammals, although there were significant sequence differences between the mouse and seal proteins in a region of the ODD domain. Some of these results indicate that seal HIF-1alpha protein can bind HIF-Ibeta, DNA, transcriptional coactivators, and von Hippel-Lindau protein (pVHL). The presence of HIF-1alpha in seal tissues was not related to the absence of pVHL, which was found to be present in all seal tissues examined. It is concluded that seal HIF-1alpha may act as a transcriptional activator and that its presence in seal tissues is probably not caused by its inability to interact with pVHL. It is suggested that seal HIF-1 may serve two functions in the postdiving period, namely, to attenuate ischemia/reperfusion-induced oxidative stress and to allow efficient lung reinflation.

Bacterially produced human HIF-1α is competent for heterodimerization and specific DNA-binding

Hypoxia-inducible factor 1alpha (HIF-1alpha) is the regulatory subunit of HIF-1, the transcriptional activator and key mediator of the cellular response to hypoxia. Regulation of HIF-1alpha occurs at multiple levels and involves several different post-translational modifications. In order to examine the importance of these modifications for the basic function of HIF-1alpha, we have produced in bacteria recombinant full-length human HIF-1alpha using different expression systems. We show that this unmodified form of HIF-1alpha is able to form a stable heterodimer with the second subunit of HIF-1 (HIF-1beta or ARNT) when both proteins are co-expressed in Escherichia coli. Furthermore, this bacterially reconstituted heterodimer exhibits specific DNA-binding activity. These data indicate that post-translational modification of HIF-1alpha is not essential for its interaction with ARNT and DNA, and provide an in vitro system for the characterization of the molecular properties of HIF-1alpha.

Oxygen-dependent gene expression in fishes

The role of oxygen in regulating patterns of gene expression in mammalian development, physiology, and pathology has received increasing attention, especially after the discovery of the hypoxia-inducible factor (HIF), a transcription factor that has been likened to a "master switch" in the transcriptional response of mammalian cells and tissues to low oxygen. At present, considerably less is known about the molecular responses of nonmammalian vertebrates and invertebrates to hypoxic exposure. Because many animals live in aquatic habitats that are variable in oxygen tension, it is relevant to study oxygen-dependent gene expression in these animals. The purpose of this review is to discuss hypoxia-induced gene expression in fishes from an evolutionary and ecological context. Recent studies have described homologs of HIF in fish and have begun to evaluate their function. A number of physiological processes are known to be altered by hypoxic exposure of fish, although the evidence linking them to HIF is less well developed. The diversity of fish presents many opportunities to evaluate if inter- and intraspecific variation in HIF structure and function correlate with hypoxia tolerance. Furthermore, as an aquatic group, fish offer the opportunity to examine the interactions between hypoxia and other stressors, including pollutants, common in aquatic environments. It is possible, if not likely, that results obtained by studying the molecular responses of fish to hypoxia will find parallels in the oxygen-dependent responses of mammals, including humans. Moreover, novel responses to hypoxia could be discovered through studies of this diverse and species-rich group.

Inactivation of the arylhydrocarbon receptor nuclear translocator (Arnt) suppresses von Hippel-Lindau disease-associated vascular tumors in mice

Patients with germ line mutations in the VHL tumor suppressor gene are predisposed to the development of highly vascularized tumors within multiple tissues. Loss of pVHL results in constitutive activation of the transcription factors HIF-1 and HIF-2, whose relative contributions to the pathogenesis of the VHL phenotype have yet to be defined. In order to examine the role of HIF in von Hippel-Lindau (VHL)-associated vascular tumorigenesis, we utilized Cre-loxP-mediated recombination to inactivate hypoxia-inducible factor-1alpha (Hif-1alpha) and arylhydrocarbon receptor nuclear translocator (Arnt) genes in a VHL mouse model of cavernous liver hemangiomas and polycythemia. Deletion of Hif-1alpha did not affect the development of vascular tumors and polycythemia, nor did it suppress the increased expression of vascular endothelial growth factor (Vegf) and erythropoietin (Epo). In contrast, phosphoglycerokinase (Pgk) expression was substantially decreased, providing evidence for target gene-dependent functional redundancy between different Hif transcription factors. Inactivation of Arnt completely suppressed the development of hemangiomas, polycythemia, and Hif-induced gene expression. Here, we demonstrate genetically that the development of VHL-associated vascular tumors in the liver depends on functional ARNT. Furthermore, we provide evidence that individual HIF transcription factors may play distinct roles in the development of specific VHL disease manifestations.

The VHL tumor suppressor in development and disease: functional studies in mice by conditional gene targeting

The von Hippel-Lindau tumor suppressor pVHL plays a critical role in the pathogenesis of familial and sporadic clear cell carcinomas of the kidney and hemangioblastomas of the retina and central nervous system. pVHL targets the oxygen sensitive alpha subunit of hypoxia-inducible factor (HIF) for proteasomal degradation, thus providing a direct link between tumorigenesis and molecular pathways critical for cellular adaptation to hypoxia. Cell type specific gene targeting of VHL in mice has demonstrated that proper pVHL mediated HIF proteolysis is fundamentally important for survival, proliferation and differentiation of many cell types and furthermore, that inactivation of pVHL may, unexpectedly, inhibit tumor growth under certain conditions. Mouse knock out studies have provided novel mechanistic insights into VHL associated tumorigenesis and established a central role for HIF in the development of the VHL phenotype.

Conservation and specialization in PAS domain dynamics

The PAS (Per-ARNT-Sim) superfamily is presented as a well-suited study case to demonstrate how comparison of functional motions among distant homologous proteins with conserved fold characteristics may give insight into their functional specialization. Based on the importance of structural flexibility of the receptive structures in anticipating the signal-induced conformational changes of these sensory systems, the dynamics of these structures were analysed. Molecular dynamics was proved to be an effective method to obtain a reliable picture of the dynamics of the crystal structures of HERG, phy3, PYP and FixL, provided that an extensive conformational space sampling is performed. Other reliable sources of dynamic information were the ensembles of NMR structures of hPASK, HIF-2alpha and PYP. Essential dynamics analysis was successfully employed to extract the relevant information from the sampled conformational spaces. Comparison of motion patterns in the essential subspaces, based on the structural alignment, allowed identification of the specialized region in each domain. This appears to be evolved in the superfamily by following a specific trend, that also suggests the presence of a limited number of general solutions adopted by the PAS domains to sense external signals. These findings may give insight into unknown mechanisms of PAS domains and guide further experimental studies.

Effect of TCDD on mRNA expression of genes encoding bHLH/PAS proteins in rat hypothalamus

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) brings about a wide variety of toxic and biochemical effects via an AH receptor (AHR)-mediated signalling pathway. Wasting syndrome and acute lethality are TCDD-induced endpoints showing a striking sensitivity difference between two rat strains, TCDD-sensitive Long-Evans (Turku/AB) (L-E) and TCDD-resistant Han/Wistar (Kuopio) (H/W). These rat strains were used to study hypothalamic effects of TCDD on expression of genes encoding AHR-regulated bHLH/PAS proteins potentially involved in molecular pathogenesis of the wasting syndrome. In addition, two well-established target genes of TCDD, CYP1A1 and CYP1A2 were also examined. Quantitative RT-PCR was used to measure mRNA levels in hypothalamus, which is a major center of food intake and body weight regulation. At both 6 and 96 h after a single dose of 50 microg/kg TCDD, significant elevations were found in mRNA levels of AHR repressor (AHRR), CYP1A1 and CYP1A2, but not those of AHR, ARNT or ARNT2. Likewise, TCDD (100 microg/kg) did not alter the expression of SIM1, implicated in the suppressive impact of TCDD on food intake, nor that of PER2, involved in regulation of circadian rhythms. Differences between H/W and L-E rats appeared in constitutive levels of AHR and ARNT and in TCDD-induced levels of CYP1A2, AHRR, AHR and ARNT, which all were about two- to four-fold lower in H/W rats. Thus, although the changes found do not account for the wasting syndrome, expression of all principal genes of the AHR-signalling pathway in rat hypothalamus make it a candidate target for TCDD.

Induced alpha-helix structure in the aryl hydrocarbon receptor transactivation domain modulates protein-protein interactions

The aryl hydrocarbon receptor (AhR) is an intracellular receptor protein that regulates gene transcription in response to both man-made and natural ligands. A modular transactivaton domain (TAD) has been mapped to the 304 C-terminal amino acids and consists of acidic, Q-rich, and P/S/T-rich subdomains. We have used steady-state intrinsic tryptophan fluorescence and circular dichroism spectroscopy to investigate the conformation of the acidic Q-rich region. The results reveal that this region of the protein is structurally flexible but adopts a more folded conformation in the presence of the natural osmolyte trimethylamine N-oxide (TMAO) and the solvent trifluoroethanol (TFE). In protein-protein interaction studies, the acidic Q-rich region bound to components of the general transcription machinery [TATA-binding protein (TBP), TAF4, and TAF6] as well as the coactivator proteins SRC-1a and TIF2. The binding site for TBP mapped to the acidic subdomain, while SRC-1a bound preferentially to the Q-rich sequence. Significantly, the binding of TBP was modulated by induced folding of the TAD with TMAO. The results indicate that the AhR TAD makes multiple interactions with the transcriptional machinery and protein conformation plays a critical role in receptor function. Taken together, these findings support a role for protein folding in AhR action and suggest possible mechanisms of receptor-dependent gene activation.

The hypoxia-inducible factor and tumor progression along the angiogenic pathway

The hypoxia-inducible factor (HIF) is a transcription factor that plays a key role in the response of cells to oxygen levels. HIF is a heterodimer of alpha- and beta-subunits where the alpha-subunit is translated constitutively but has a very short half-life under normal oxygen concentrations. Negative regulation of the half-life and activity of the alpha-subunit is dependent on its posttranslational hydroxylation by hydroxylases that are dependent on oxygen for activity. Thus under low oxygen (hypoxic) conditions the hydroxylases are inactive and the alpha-subunit is stable and able to interact with the beta-subunit to bind and induce transcription of target genes. Hypoxic conditions are encountered in development and in disease states such as cancer. Tumors that have outstripped their blood supply become hypoxic and express high levels of HIF. HIF in turn targets genes that induce survival, glycolysis, and angiogenesis, a form of neovascularization, which ensures the tumor with a continued supply of oxygen and nutrients for further growth.

Effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and leptin on hypothalamic mRNA expression of factors participating in food intake regulation in a TCDD-sensitive and a TCDD-resistant rat strain

An acutely toxic dose of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) leads to a drastically and permanently reduced feed intake and wasting by an unknown mechanism. We focused on the possible interference of TCDD with hypothalamic factors known to take part in the regulation of eating and metabolism, utilizing the over 1000-fold TCDD-sensitivity difference between Long-Evans (Turku/AB; L-E) and Han/Wistar (Kuopio) rats. The mRNA expression of 18 hypothalamic factors (including NPY, AgRP, and CART) was measured by quantitative RT-PCR at 6, 24 and 96 h after TCDD administration. The effects of TCDD were compared with those of leptin and with feed restriction employing a TCDD dose that elicited a severe reduction of feed intake in L-E rats. TCDD mainly modified expression of orexigenic factors causing an initial suppression followed by reversal to enhanced expression by 96 h. The latter was also seen in feed-restricted controls. In contrast, leptin altered both orexigenic and anorexigenic factor mRNAs in a more even manner and its effects were clustered at 6 h. The transient nature of feeding-promoting factor suppression does not strongly support a key role for this phenomenon in TCDD-induced wasting syndrome. However, the fact that TCDD mainly affected orexigenic factors and the temporal differences in response found between the rat strains warrant further research.

Induction of cyclin D2 in rat granulosa cells requires FSH-dependent relief from FOXO1 repression coupled with positive signals from Smad

Ovarian follicles undergo exponential growth in response to follicle-stimulating hormone (FSH), largely as a result of the proliferation of granulosa cells (GCs). In vitro under serum-free conditions, rat GCs differentiate in response to FSH but do not proliferate unless activin is also present. In the presence of FSH plus activin, GCs exhibit enhanced expression of cyclin D2 as well as inhibin-alpha, aromatase, steroidogenic factor-1 (SF-1), cholesterol side chain (SCC), and epiregulin. In this report we sought to identify the signaling pathways by which FSH and activin promote GC proliferation and differentiation. Our results show that these responses are associated with prolonged Akt phosphorylation relative to time-matched controls and are dependent on phosphatidylinositol 3-kinase (PI 3-kinase) and Smad2/3 signaling, based on the ability of the PI 3-kinase inhibitor LY294002 or infection with adenoviral dominant negative Smad3 (DN-Smad3) mutant to attenuate induction of cyclin D2, inhibin-alpha, aromatase, SCC, SF-1, and epiregulin. The DN-Smad3 mutant also abolished prolonged Akt phosphorylation stimulated by FSH plus activin 24 h post-treatment. Infection with the adenoviral constitutively active forkhead box-containing protein, O subfamily (FOXO)1 mutant suppressed induction of cyclin D2, aromatase, inhibin-alpha, SF-1, and epiregulin. Transient transfections of GCs with constitutively active FOXO1 mutant also suppressed cyclin D2, inhibin-alpha, and epiregulin promoter-reporter activities. Chromatin immunoprecipitation results demonstrate in vivo the association of FOXO1 with the cyclin D2 promoter in untreated GCs and release of FOXO1 from the cyclin D2 promoter upon addition of FSH plus activin. These results suggest that proliferation and differentiation of GCs in response to FSH plus activin requires both removal of FOXO1-dependent repression and positive signaling from Smad2/3.

L-gamma-Glutamyl-L-cysteinyl-glycine (glutathione; GSH) and GSH-related enzymes in the regulation of pro- and anti-inflammatory cytokines: a signaling transcriptional scenario for redox(y) immunologic sensor(s)?

Of the antioxidant/prooxidant mechanisms mediating the regulation of inflammatory mediators, particularly cytokines, oxidative stress-related pathways remain a cornerstone. It is conspicuous that there is a strong association between free radical accumulation (ROS/RNS; oxidative stress) and the evolution of inflammation and inflammatory-related responses. The scenario that upholds a consensus on the aforementioned is still evolving to unravel, from an immunologic perspective, the molecular mechanisms associated with ROS/RNS-dependent inflammation. Cytokines are keynote players when it comes to defining an intimate relationship among reduction-oxidation (redox) signals, oxidative stress and inflammation. How close we are to identifying the molecular basis of this intricate association should be weighed against the involvement of specific signaling molecules and, potentially, transcription factors. L-gamma-Glutamyl-L-cysteinyl-glycine, or glutathione (GSH), an antioxidant thiol, has shaped, and still is refining, the face of oxidative signaling in terms of regulating the milieu of inflammatory mediators, ostensibly via the modulation (expression/repression) of oxygen- and redox-responsive transcription factors, hence termed redox(y)-sensitive cofactors. When it comes to the arena of oxygen sensing, oxidative stress and inflammation, nuclear factor-kappaB (NF-kappaB) and hypoxia-inducible factor-1alpha (HIF-1alpha) are key players that determine antioxidant/prooxidant responses with oxidative challenge. It is the theme therein to underlie current understanding of the molecular association hanging between oxidative stress and the evolution of inflammation, walked through an elaborate discussion on the role of transcription factors and cofactors. Would that classify glutathione and other redox signaling cofactors as potential anti-inflammatory molecules emphatically remains of particular interest, especially in the light of identifying upstream and downstream molecular pathways for conceiving therapeutic, alleviating strategy for oxidant-mediated, inflammatory-related disease conditions.

Non-hypoxic transcriptional activation of the aryl hydrocarbon receptor nuclear translocator in concert with a novel hypoxia-inducible factor-1alpha isoform

Aryl hydrocarbon receptor nuclear translocator (ARNT) belongs to the basic helix-loop-helix Per-Arnt-Sim (bHLH PAS) protein which dimerizes with other PAS proteins. Although it has a transactivation domain (TAD), ARNT functions as an assistant partner of main factors, such as aryl hydrocarbon receptor and hypoxia-inducible factors, rather than acting as a straightforward transcription factor. However, ARNT may function as an active transcription factor using its TAD either in association with itself, single-minded protein 1, or trachealess protein. In the present study, we identified a novel ARNT partner, a HIF-1alpha variant, which is ubiquitously expressed in human tissues and cancer cell lines. The HIF-1alpha variant, designated HIF-1alpha417, bound to ARNT and, moreover, stimulated the transcription of the erythropoietin enhancer reporter gene. This stimulation was markedly augmented by ARNT but not by the ARNT603 mutant lacking the TAD. Thus, augmentation by ARNT suggests that ARNT determined the transcriptional activity. HIF-1alpha417 was found to be associated with ARNT and to bind to the hypoxia response element containing the E-box core. Moreover, HIF-1alpha417 promoted the nuclear translocation of ARNT, and conversely ARNT stabilized HIF-1alpha417. Taken together, our results suggest that HIF-1alpha417 is a novel partner that is required for transcription activity of ARNT.

The Aryl Hydrocarbon (Ah) Receptor Transcriptional Regulator Hepatitis B Virus X-associated Protein 2 Antagonizes p23 Binding to Ah Receptor-Hsp90 Complexes and Is Dispensable for Receptor Function

To further understand the role that the hepatitis B virus X-associated protein 2 (XAP2) plays in regulating aryl hydrocarbon receptor (AhR) function, a point mutation was introduced at tyrosine 408 of the AhR, changing the residue to an alanine or lysine. These mutations resulted in the loss of AhR binding to endogenous XAP2 in COS-1 cells and reduced binding of exogenously expressed XAP2. Cellular localization of the mutant AhR-yellow fluorescent protein fusion proteins remained nuclear when XAP2 was co-expressed, while the non-mutant receptor was redistributed to the cytoplasm. XAP2 expression caused an overall repression of constitutive and ligand-induced AhR transcriptional activity. However, increased expression of XAP2 had no effect on the AhRY408A mutant transcriptional activity. Additionally the XAP2 binding-deficient AhR mutants showed overall higher transcriptional activity when compared with the non-mutant receptor. Interestingly reduced incorporation of the Hsp90 associated co-chaperone p23 in the unliganded AhR complex was observed with increasing XAP2 expression. The displacement of p23 from Hsp90 did not occur when increasing levels of XAP2 were introduced in COS-1 cells in the absence of the AhR; thus this displacement event occurs specifically within an AhR complex. Finally XAP2 itself was capable of existing in multimeric complexes, and these complexes did not require Hsp90 or AhR to form. However, it is not yet clear whether XAP2 can exist within the AhR complex in more than one copy.

Hypoxia-dependent regulation of PHD1: cloning and characterization of the human PHD1/EGLN2 gene promoter

The recent identification of hypoxia-inducible-factor (HIF) prolyl hydroxylases (PHD1, 2, and 3), which modify HIF-1 alpha in an oxygen-dependent manner, provided an important link between oxygen availability and hypoxia-induced gene expression. However, little is known about the regulation of the PHDs. To investigate the transcriptional regulation of PHD1, we cloned the PHD1 gene promoter. Here, we report that the expression of PHD1 is reduced under hypoxic conditions. Furthermore, we identified binding sites for aryl hydrocarbon nuclear translocator (ARNT/HIF-1 beta) within the PHD1 promoter, and showed that ARNT is associated in vivo with the PHD1 promoter following hypoxia, which implies a role for ARNT in the hypoxia-dependent regulation of PHD1. Taken together, our findings suggest a hypoxia-induced regulatory loop of PHD1 expression, mediated by ARNT.

An overview of the basic helix-loop-helix proteins

The basic helix-loop-helix proteins, dimeric transcription factors, are found in almost all eukaryotes and in animals are important regulators of embryonic development.

The basic helix-loop-helix proteins are dimeric transcription factors that are found in almost all eukaryotes. In animals, they are important regulators of embryonic development, particularly in neurogenesis, myogenesis, heart development and hematopoiesis.